> ## Documentation Index
> Fetch the complete documentation index at: https://docs.cosmosid.com/llms.txt
> Use this file to discover all available pages before exploring further.

# What is Cosmos-Hub 2.0

<img src="https://mintcdn.com/cmbio/1bkEKvEMzn3OLKqg/logo/dark.svg?fit=max&auto=format&n=1bkEKvEMzn3OLKqg&q=85&s=d0761cd0ad078897e0e627c55375d649" alt="Cosmos-Hub" style={{ width: "46%" }} className="mx-auto" width="2134" height="667" data-path="logo/dark.svg" />

<p style={{ textAlign: "center", fontSize: "1.3rem", fontWeight: 600, marginTop: "0.75rem" }}>
  One platform, from raw sequence to scientific decision.
</p>

Cosmos-Hub 2.0 is a centralized omics operating system. It gives scientists, bioinformaticians, and R\&D teams one governed platform for turning omics data into scientific insight. Instead of scattering the building blocks of omics research across separate tools, it keeps them in one shared environment: data and metadata, pipelines, analysis, AI tools, a collaboration workspace, and exports. The result is a workflow that is easier to manage, reproduce, and share.

<CardGroup cols={2}>
  <Card title="Take the Quickstart" icon="forward" href="DAP_docs/quickstart">
    Go from sign-in to exported results in a few steps.
  </Card>

  <Card title="Get access" icon="envelope" href="mailto:info@cosmos-hub.com">
    See Cosmos-Hub 2.0 running on your own data.
  </Card>
</CardGroup>

## The challenge of microbiome multi-omics

Microbiome multi-omics resources tend to be spread across many tools. You store sequencing data in one place, run pipelines in another, write separate scripts for statistics, and reach for yet more tools to create figures and share results. Along the way, data ends up in silos, file versions drift, and projects stall in the handoffs between bench and bioinformatics teams. Often the coordination becomes harder than the science itself. Cosmos-Hub 2.0 brings these steps into one platform, so your data, analyses, and results stay connected from start to finish.

## Why Cosmos-Hub 2.0

Cosmos-Hub 2.0 rests on three layers that build on each other: a **unified data foundation**, **no-code analysis at expert depth** that runs on top of it, and **governance** that turns every result into shared, reusable knowledge.

<CardGroup cols={3}>
  <Card title="Raw sequence to decision, in one platform" icon="diagram-project">
    One governed platform. All your microbiome data, profiling workflows, a queryable database for all your profiles, advanced statistical models, AI tools, and collaboration — in one place. Your tools, data, assets, and people work together on a single platform.
  </Card>

  <Card title="No-code science at expert depth" icon="wand-magic-sparkles">
    Turn your raw microbial 'omics data into ready-to-use profiles with our award-winning Cosmos-Hub Workflows. Then unlock publication-ready insights in Analysis Studio — an interactive toolbox for microbiome analyses, statistical tests, and machine learning. No coding required. No compromise on scientific rigor.
  </Card>

  <Card title="Every study becomes institutional knowledge" icon="boxes-stacked">
    Each analysis becomes a governed, shareable study. One-off results turn into a lasting asset that stays reproducible, can be benchmarked against the Cmbio Atlas and its 150,000+ datasets, and retains traceability and therefore value even when people or projects move on.
  </Card>
</CardGroup>

## Key features and capabilities

* **Organize omics projects in one governed workspace.** Keep data, metadata, analyses, results, collaborators, and exports connected inside structured workspaces and studies.
* **Process raw sequencing data with validated pipelines.** Run Cosmos-Hub profiling workflows directly in the platform, including CHAMP, Kepler, DADA2 short-read amplicon profiling, and EMU long-read profiling.
* **Perform analyses on multiple omics data types under one system.** Work with shotgun metagenomics, 16S/ITS amplicon data, metatranscriptomics, metabolomics, proteomics, and custom feature tables.
* **Find and assemble the right data faster.** Use AI-supported data access to turn scientific questions into queries that select the relevant samples, tables, and metadata.
* **Analyze data without writing code.** Explore patterns, compare groups, test hypotheses, run statistical workflows, build models, and generate figures in a flexible no-code Analysis Studio.
* **Benchmark studies against reference data.** Use the Cmbio Atlas to place your results in a broader biological context and to compare your studies against a large, harmonized reference dataset.
* **Create reproducible, shareable results.** Save snapshots, track versions, preserve provenance, and export analysis outputs, so results can be revisited, audited, shared, and trusted.
* **Collaborate securely across teams.** Manage access with roles, permissions, SSO/MFA, and GDPR-aligned infrastructure, so data and results stay governed as projects grow.

### The Analysis Studio

The Analysis Studio is a single no-code studio that covers the whole microbiome analytical workflow. You can run statistics, train machine-learning models, and build figures in the same interface, with customizable parameters and interactive visualizations throughout.

<CardGroup cols={2}>
  <Card title="No-code interface" icon="sliders">
    Point-and-click analyses with customizable parameters that put full control in the hands of non-programmers.
  </Card>

  <Card title="Microbiome statistics" icon="chart-mixed">
    Alpha and beta diversity, PCA and PERMANOVA, rarefaction, and differential abundance and prevalence testing, with multiple-testing correction.
  </Card>

  <Card title="Machine-learning toolbox" icon="robot">
    Predict and classify from microbiome profiles, with feature importance to highlight the taxa or functions that distinguish a group. Methods include Random Forest, Logistic Regression, SVM, and Gradient Boosting.
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  <Card title="Publication-ready visualizations" icon="chart-column">
    Diversity and ordination plots, heatmaps, stacked bar charts, and volcano and forest plots.
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## How it works

Cosmos-Hub 2.0 is organized as a simple hierarchy that mirrors how microbiome R\&D teams work:

* **Workspace.** The home for a team, such as a department or research unit. Workspaces make collaboration between team members easier.
* **Study.** One project's data in one place: feature tables, microbial profiles, metadata, analyses, and any assets relevant to your project.
* **AI Query Builder.** A lot of time in microbiome research is spent building the right cohort of data to analyze — metadata wrangling, SQL queries, filtering, sample matching. The AI Query Builder facilitates all of this, helping you select a targeted subset of a study, including samples, tables, groups, and metadata, that an analysis should run on.
* **Analysis modules.** Turn a cohort into results, using the Analysis Studio and its modules for diversity, ordination, differential abundance, and machine learning to quickly translate data into scientific insights.
* **Snapshots and export.** Save the parameters and results of each step and keep a record of all your team's work. Collaborating on analyses and making every step reproducible has never been easier. Once you get to the figure you need, export it and it's ready to be used in your reports or a slide deck.

<Card title="Take the Quickstart" icon="forward" href="https://docs.cosmosid.com/DAP_docs/quickstart">
  Go from sign-in to exported results in a few steps.
</Card>